TBAE

Publications

2025

Entropy driven inductive response of topological insulators

Authors: A. Mert Bozkurt, Sofie Kölling, Alexander Brinkman, İnanç Adagideli
Place of Publication: SciPost Phys.
Publication Type: Journal Article

2024

Factors Affecting the Electron Conductivity in Single Crystal Li7La3Zr2O12 and Li7P3S11

Authors: Samet Demir, Adem Tekin, Yu-Te Chan, Christoph Scheurer, Karsten Reuter, Alan C. Luntz and Johannes Voss
Place of Publication: New Journal of Physics
Publication Type: Journal Article

Signature of topology via heat transfer analysis in the Su-Schrieffer-Heeger (SSH) model

Authors: Vipul Upadhyay, M. Tahir Naseem, Özgür E. Müstecaplıoğlu and Rahul Marathe
Place of Publication: New Journal of Physics
Publication Type: Journal Article

Prospects for γ-ray observations of the Perseus galaxy cluster with the Cherenkov Telescope Array

Authors: Abe, Koya, et al.
Place of Publication: Journal of cosmology and astroparticle physics
Publication Type: Journal Article

Mixing thermal coherent states for precision and range enhancement in quantum thermometry

Authors: Asghar Ullah, M. Tahir Naseem and Özgür E. Müstecaplıoğlu
Place of Publication: Quantum Science and Technology
Publication Type: Journal Article

Prospects for a survey of the galactic plane with the Cherenkov Telescope Array

Authors: Abe, Shinsuke, et al.
Place of Publication: Journal of Cosmology and Astroparticle Physics
Publication Type: Journal Article

PHACTboost: A Phylogeny-Aware Pathogenicity Predictor for Missense Mutations via Boosting

Authors: Onur Dereli, Nurdan Kuru, Emrah Akkoyun, Aylin Bircan, Oznur Tastan, Ogün Adebali
Place of Publication: Molecular Biology and Evolution
Publication Type: Journal Article

Conditions on detecting tripartite entangled state in psychophysical experiments

Authors: Lea Gassab, Ali Pedram and Özgür E. Müstecaplıoğlu
Place of Publication: EPJ Plus
Publication Type: Journal Article

Light-Harvesting Lead-Free Mixed Cation Hybrid Halide Perovskites: A Density Functional Theory-Based Computational Screening Study

Authors: Somayyeh Alidoust, Fatemeh Jamalinabijan, Adem Tekin
Place of Publication: ACS Applied Energy Materials
Publication Type: Journal Article

Cross-species investigation into the requirement of XPA for nucleotide excision repair

Authors: Cansu Kose, Xuemei Cao, Evan B Dewey, Mustafa Malkoç, Ogün Adebali, Jeff Sekelsky, Laura A. Lindsey-Boltz, Aziz Sancar
Place of Publication: Nucleic Acids Research
Publication Type: Journal Article

Phase Prediction via Crystal Structure Similarity in the Periodic Number Representation

Authors: Cem Oran, Riccarda Caputo, Pierre Villars, Hasan Bilal Özcü, Feraye Hatice Canbaz, Adem Tekin
Place of Publication: Inorganic Chemistry
Publication Type: Journal Article

Quantum estimation of the stokes vector rotation for a general polarimetric transformation

Authors: Ali Pedram, Vira R Besaga, Lea Gassab, Frank Setzpfandt and Özgür E. Müstecaplıoğlu
Place of Publication: New Journal of Physics
Publication Type: Journal Article

Dynamics of transcription-coupled repair of cyclobutane pyrimidine dimers and (6-4) photoproducts in Escherichia coli

Authors: Ogϋn Adebali, Aziz Sancar, and Christopher P. Selby
Place of Publication: PNAS
Publication Type: Journal Article

Quantum scars and caustics in Majorana billiards

Authors: R. Johanna Zijderveld, A. Mert Bozkurt, Michael Wimmer, Inanc Adagideli
Place of Publication: SciPost Physics
Publication Type: Journal Article

Nonlocality Enhanced Precision in Quantum Polarimetry via Entangled Photons

Authors: Ali Pedram, Vira R. Besaga, Frank Setzpfandt, Ozgur E. Müstecaplioglu
Place of Publication: Advanced Quantum Technologies
Publication Type: Journal Article

Optimization of CHARMM force field parameters for ryanodine receptor inhibitory drug dantrolene using FFTK and FFParam

Authors: Saliha Nur Uludag, Cemil Can Saylan, Adem Tekin & Sefer Baday
Place of Publication: Journal of Molecular Modeling
Publication Type: Journal Article

The expected potential of hadronic PeVatron searches with spectral γ-ray data from the Southern Wide-field Gamma-ray Observatory

Authors: Ekrem Oğuzhan Angüner, Tülün Ergin
Place of Publication: Astroparticle Physics
Publication Type: Journal Article

Pybkgmodel - a background modeling toolbox for the CTA

Authors: Strzys, Marcel C., et al
Place of Publication: 38th International Cosmic Ray Conference
Publication Type: Conference Article

Engineering Four-Qubit Fuel States for Protecting Quantum Thermalization Machine from Decoherence

Authors: Fatih Ozaydin, Ramita Sarkar, Veysel Bayrakci, Cihan Bayindir, Azmi Ali Altintas and Ozgur E. Müstecaplioglu
Place of Publication: Information 2024
Publication Type: Journal Article

Evolutionary history of calcium-sensing receptors unveils hyper/hypocalcemia-causing mutations

Authors: Aylin Bircan, Nurdan Kuru, Onur Dereli, Berkay Selçuk, Ogün Adebali
Place of Publication: PLOS Computational Biology
Publication Type: Journal Article

Fundamentals and Applications of Heat Currents in Quantum Systems

Authors: Naseem, M. Tahir, and Ozgur E. Müstecaplioglu
Place of Publication: International Conference on Frontiers of Fundamental Physics
Publication Type: Conference Article

2023

On the role of initial coherence in the spin phase-space entropy production rate

Authors: Giorgio Zicari, Baris Cakmak, Ozgur Esat Müstecaplioglu and Mauro Paternostro
Place of Publication: New Journal of Physics
Publication Type: Journal Article

A quantum Otto engine with shortcuts to thermalization and adiabaticity

Authors: A. Pedram, S. C. Kadıoğlu, A. Kabakçıoğlu and Ö. E. Müstecaplıoğlu
Place of Publication: New Journal of Physics
Publication Type: Journal Article

A compendious review of majorization-based resource theories: quantum information and quantum thermodynamics

Authors: Gökhan Torun, Onur Pusuluk, Özgür Esat Müstecaplıoğlu
Place of Publication: Turkish Journal of Physics
Publication Type: Journal Article

Coherence, superposition, and Löwdin symmetric orthogonalization

Authors: Gökhan Torun
Place of Publication: Journal of Physics A: Mathematical and Theoretical
Publication Type: Journal Article

Experimental and Ab-Initio Investigation of the Electrical Conductivity of Emeraldine Salt

Authors: Zeynep Ergönenç Yavas, Duygu Cevher, Hasan Töre Silis, Ali Cirpan, Oğuz Gülseren, Cesare Franchini
Place of Publication: The Journal of Physical Chemistry C
Publication Type: Journal Article

Exploring the high energy frontiers of the Milky Way with ground-based gamma-ray astronomy: PeVatrons and the quest for the origin of Galactic cosmic-rays

Authors: Ekrem Oğuzhan Angüner
Place of Publication: Turkish Journal of Physics
Publication Type: Journal Article

Hydrogen Storage in Trimetallic Borohydrides: a Crystal Structure Prediction and Ab Initio Molecular Dynamics Simulations Study

Authors: Samet Demir, Mostafa Torkashvand, Shirzad Jouybar, Zahra Nikfarjam, Farshid Zargari, Saeedeh Sarabadani Tafreshi, Adem Tekin
Place of Publication: The Journal of Physical Chemistry C
Publication Type: Journal Article

Sensitivity of the Cherenkov Telescope Array to TeV photon emission from the Large Magellanic Cloud

Authors: Acharyya, Atreya, et al.
Place of Publication: Monthly Notices of the Royal Astronomical Society
Publication Type: Journal Article

Deciphering the dynamic codes: Advances in biomolecular modeling and simulation

Authors: Gregory A Voth, Turkan Haliloglu
Place of Publication: Current opinion in structural biology
Publication Type: Journal Article

Stable and metastable crystal structures and ammonia dynamics in strontium chloride ammines

Authors: Samet Demir, Gözde İniş Demir, Mehmet Çankaya, Adem Tekin
Place of Publication: Physical Chemistry Chemical Physics
Publication Type: Journal Article

Prototype Open Event Reconstruction Pipeline for the Cherenkov Telescope Array

Authors: Maximilian Linhoff, Lukas Beiske, Noah Biederbeck, Stefan Fröse, Karl Kosack and Lukas Nicke
Place of Publication: 38th International Cosmic Ray Conference
Publication Type: Conference Article

Dynamical spin-orbit-based spin transistor

Authors: Fahriye N. Gürsoy, P. Reck, C. Gorini, K. Richter, I. Adagideli
Place of Publication: SciPost Phys.
Publication Type: Journal Article

Terrestrial Very-Long-Baseline Atomic Interferometry: Workshop Summary

Authors: Abend, S., et al.
Place of Publication: Theoretical Physics Group
Publication Type: Journal Article

Search for the Galactic accelerators of cosmic rays up to the knee with the Pevatron test statistic

Authors: Ekrem Oğuzhan Angüner, Gerrit Spengler, Elena Amato, Sabrina Casanova
Place of Publication: Monthly Notices of the Royal Astronomical Society
Publication Type: Journal Article

The interplay of 3D genome organization with UV-induced DNA damage and repair

Authors: Ümit Akköse, Ogün Adebali
Place of Publication: JBC Communication
Publication Type: Journal Article

The Mfd protein is the transcription-repair coupling factor (TRCF) in Mycobacterium smegmatis

Authors: Ogun Adebali, Yanyan Yang, Pradeep Neupane, Nneka I. Dike, Julia L. Boltz, Cansu Kose, Miriam Braunstein, Christopher P. Selby, Aziz Sancar, Laura A. Lindsey-Boltz
Place of Publication: Journal of Biological Chemistry
Publication Type: Journal Article

Downregulated NPAS4 in multiple brain regions is associated with major depressive disorder

Authors: Berkay Selcuk, Tuana Aksu, Onur Dereli & Ogun Adebali
Place of Publication: Scientific Reports
Publication Type: Journal Article

2022

Classical and quantum orbital correlations in molecular electronic states

Authors: Onur Pusuluk, Mahir H Yeşiller, Gökhan Torun, Özgür E Müstecaplıoğlu, Ersin Yurtsever and Vlatko Vedral
Place of Publication: New Journal of Physics
Publication Type: Journal Article

2D-FFCASP-A New Approach for 2D Structure Prediction Applied to Self-Assemblies of DNA Bases

Authors: Gözde İniş Demir, Samet Demir, Adem Tekin
Place of Publication: Advanced Theory and Simulations
Publication Type: Journal Article

Equiatomic binary phases of Copper-Rare Earth Elements. An overview of monocuprides from first-principles calculations

Authors: Prof. Dr. Riccarda Caputo, Cem Oran, Prof. Dr. Adem Tekin, Dr. Pierre Villars
Place of Publication: ChemPhysChem
Publication Type: Journal Article

Engineering entanglement between resonators by hot environment

Authors: M. Tahir Naseem and Özgür E. Müstecaplıoğlu
Place of Publication: Quantum Science and Technology
Publication Type: Journal Article

Quantum signatures in a quadratic optomechanical heat engine with an atom in a tapered trap

Authors: Mohsen Izadyari, Mehmet Öncü, Kadir Durak, and Özgür E. Müstecaplioğlu
Place of Publication: Journal of the Optical Society of America B
Publication Type: Journal Article

Environment-Assisted Modulation of Heat Flux in a Bio-Inspired System Based on Collision Model

Authors: Ali Pedram, Baris Cakmak and Ozgur E. Müstecaplioglu
Place of Publication: Entropy 2022
Publication Type: Journal Article

A novel phylogeny-dependent coevolution algorithm

Authors: Kuru, Nurdan and Adebali, Ogun
Place of Publication: 15th International Symposium on Health Informatics and Bioinformatics HIBIT'22
Publication Type: Conference Article

Reproducible and scalable data analysis on high performance computing

Authors: Akkoyun Emrah, Kuru Nurdan, Dereli Onur, Bircan Aylin, Taştan Öznur and Adebali Ogün
Place of Publication: 15th International Symposium on Health Informatics and Bioinformatics HIBIT'22
Publication Type: Conference Article

Effects of replication domains on genome-wide UV-induced DNA damage and repair

Authors: Yanchao Huang, Cem Azgari, Mengdie Yin, Yi-Ying Chiou, Laura A. Lindsey-Boltz, Aziz Sancar, Jinchuan Hu, Ogun Adebali
Place of Publication: PLoS genetics
Publication Type: Journal Article

2021

Crystal Structure Prediction and Dehydrogenation Mechanism of LiMg(BH4)3(NH3)2

Authors: Gözde İniş Demir, Riccarda Caputo, Samet Demir, Adem Tekin
Place of Publication: The Journal of Physical Chemistry C
Publication Type: Journal Article

FFCASP: A Massively Parallel Structure Prediction Algoritrystal Shm

Authors: Samet Demir, Adem Tekin
Place of Publication: Journal of Chemical Theory and Computation
Publication Type: Journal Article

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